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cbedtools.pyx
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cbedtools.pyx
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"""
bedtools.pyx: A Cython wrapper for the BEDTools BedFile class
Authors: Aaron Quinlan[1], Brent Pedersen[2]
Affl: [1] Center for Public Health Genomics, University of Virginia
[2]
Email: aaronquinlan at gmail dot com
"""
include "cbedtools.pxi"
from cython.operator cimport dereference as deref
from pybedtools.helpers import parse_attributes
cdef class Interval:
cdef BED *_bed
def __init__(self, chrom, start, end, strand=None):
if strand is None:
self._bed = new BED(string(chrom), start, end)
else:
self._bed = new BED(string(chrom), start, end, string(strand))
def get_chrom(self):
return self._bed.chrom.c_str()
def set_chrom(self, chrom):
self._bed.chrom = string(chrom)
chrom = property(get_chrom, set_chrom)
def get_start(self):
return self._bed.start
def set_start(self, int start):
self._bed.start = start
start = property(get_start, set_start)
def get_end(self):
return self._bed.end
def set_end(self, int end):
self._bed.end = end
stop = end = property(get_end, set_end)
# TODO: make this more robust.
@property
def count(self):
return int(self.other[-1])
@property
def name(self):
if self._bed.isGff:
return parse_attributes(self._bed.fields[8].c_str())["ID"]
elif self._bed.isVcf:
raise Exception("not implemented")
else:
return self._bed.name.c_str()
@property
def score(self):
return self._bed.score.c_str()
@property
def strand(self):
return self._bed.strand.c_str()
@property
def other(self):
return string_vec2list(self._bed.otherFields)
@property
def length(self):
return self._bed.end - self._bed.start
# TODO: maybe bed.overlap_start or bed.overlap.start ??
@property
def o_start(self):
return self._bed.o_start
@property
def o_end(self):
return self._bed.o_end
@property
def o_amt(self):
return self._bed.o_end - self._bed.o_start
def __str__(self):
return self._bed.reportBed().c_str()
def __repr__(self):
return "Interval(%s:%i-%i)" % (self.chrom, self.start, self.end)
def __dealloc__(self):
del self._bed
def __len__(self):
return self._bed.end - self._bed.start
def __getitem__(self, object key):
cdef int i
if isinstance(key, (int, long)):
if key >= self._bed.fields.size():
raise IndexError('field index out of range')
return self._bed.fields.at(key).c_str()
elif isinstance(key, slice):
return [self._bed.fields.at(i).c_str() for i in \
range(key.start or 0,
key.stop or self._bed.fields.size(),
key.step or 1)]
elif isinstance(key, basestring):
return getattr(self, key)
cdef Interval create_interval(BED b):
cdef Interval pyb = Interval.__new__(Interval)
pyb._bed = new BED(b.chrom, b.start, b.end, b.name,
b.score, b.strand, b.otherFields,
b.o_start, b.o_end, b.bedType, b.isGff, b.isVcf, b.status)
pyb._bed.fields = b.fields
return pyb
cdef Interval create_interval_from_list(list fields):
cdef Interval pyb = Interval.__new__(Interval)
pyb._bed = new BED(string(fields[0]), int(fields[1]), int(fields[2]), string(fields[3]),
string(fields[4]), string(fields[5]), list_to_vector(fields[6]))
return pyb
cdef vector[string] list_to_vector(list li):
cdef vector[string] s
cdef int i
for i in range(len(li)):
s.push_back(string(li[i]))
return s
cdef list string_vec2list(vector[string] sv):
cdef size_t size = sv.size(), i
return [sv.at(i).c_str() for i in range(size)]
cdef list bed_vec2list(vector[BED] bv):
cdef size_t size = bv.size(), i
cdef list l = []
cdef BED b
for i in range(size):
b = bv.at(i)
l.append(create_interval(b))
return l
def overlap(int s1, int s2, int e1, int e2):
return min(e1,e2) - max(s1,s2)
cdef class IntervalFile:
cdef BedFile *intervalFile_ptr
cdef bint _loaded
cdef bint _open
def __init__(self, intervalFile):
self.intervalFile_ptr = new BedFile(string(intervalFile))
self._loaded = 0
self._open = 0
def __dealloc__(self):
del self.intervalFile_ptr
def __iter__(self):
return self
def __next__(self):
if not self._open:
self.intervalFile_ptr.Open()
self._open = 1
cdef BED b = self.intervalFile_ptr.GetNextBed()
if b.status == BED_VALID:
return create_interval(b)
elif b.status == BED_INVALID:
raise StopIteration
else:
return self.next()
def loadIntoMap(self):
if self._loaded: return
self.intervalFile_ptr.loadBedFileIntoMap()
self._loaded = 1
def all_hits(self, Interval interval, bool same_strand=False, float overlap=0.0):
"""
Search for the "bed" feature in this file and ***return all overlaps***
"""
cdef vector[BED] vec_b
self.loadIntoMap()
if same_strand == False:
vec_b = self.intervalFile_ptr.FindOverlapsPerBin(deref(interval._bed), overlap)
try:
return bed_vec2list(vec_b)
finally:
pass
else:
vec_b = self.intervalFile_ptr.FindOverlapsPerBin(deref(interval._bed), same_strand, overlap)
try:
return bed_vec2list(vec_b)
finally:
pass
# search() is an alias for all_hits
search = all_hits
def any_hits(self, Interval interval, bool same_strand=False, float overlap=0.0):
"""
Search for the "bed" feature in this file and return
whether (True/False) >= 1 overlaps are found.
"""
found = 0
self.loadIntoMap()
if same_strand == False:
found = self.intervalFile_ptr.FindAnyOverlapsPerBin(deref(interval._bed), overlap)
else:
found = self.intervalFile_ptr.FindAnyOverlapsPerBin(deref(interval._bed), same_strand, overlap)
return found
def count_hits(self, Interval interval, bool same_strand=False, float overlap=0.0):
"""
Search for the "bed" feature in this file and return the *** count of hits found ***
"""
self.loadIntoMap()
if same_strand == False:
return self.intervalFile_ptr.CountOverlapsPerBin(deref(interval._bed), overlap)
else:
return self.intervalFile_ptr.CountOverlapsPerBin(deref(interval._bed), same_strand, overlap)